rs9295592

Variant names:

• chr6-23518043-T-C
• rs9295592
• ENST00000690652.3:n.356-60373A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690652.3(ENSG00000289368):​n.356-60373A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,948 control chromosomes in the GnomAD database, including 23,138 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (23138 hom., cov: 31)
• Consequence: ENSG00000289368 ENST00000690652.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 3 publications found

Genes affected

ENSG00000289368 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374976	XR_001744046.2	n.401-60373A>G		intron_variant	Intron 3 of 6
LOC105374976	XR_007059501.1	n.379-60373A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289368	ENST00000690652.3	n.356-60373A>G		intron_variant	Intron 1 of 2
ENSG00000289368	ENST00000700866.2	n.181-60373A>G		intron_variant	Intron 1 of 2
ENSG00000289368	ENST00000702216.2	n.203-60373A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83306 AN: 151830 Hom.: 23105 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.540

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.549 AC: 83394 AN: 151948 Hom.: 23138 Cov.: 31 AF XY: 0.545 AC XY: 40479 AN XY: 74260

African (AFR) AF: 0.600 AC: 24851 AN: 41440

American (AMR) AF: 0.473 AC: 7213 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2238 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1748 AN: 5148

South Asian (SAS) AF: 0.488 AC: 2347 AN: 4808

European-Finnish (FIN) AF: 0.550 AC: 5810 AN: 10556

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37381 AN: 67956

Other (OTH) AF: 0.545 AC: 1151 AN: 2110

Alfa AF: 0.541 Hom.: 9324

Bravo AF: 0.543

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.59
PhyloP100		-0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9295592; hg19: chr6-23518271; COSMIC: COSV66848353;